Starting
Initialising…
0%
VHL
Final classification
Benign
VHL c.-77C>T · p.?
VHL

NM_000551.3:c.-77C>T meets BA1 (Stand-Alone) under VHL VCEP v1.1.0: GroupMax Filtering Allele Frequency of 8.88% in gnomAD v4.1 far exceeds the BA1 threshold of 0.0156%, establishing this variant as benign.

Gene
VHL
Transcript
NM_000551.3
HGVS · transcript:coding
NM_000551.3:c.-77C>T
Consequence
N/A
GRCh38
chr3:10141771 C>T
GRCh37
chr3:10183455 C>T
Basis ClinGen VHL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VHL Version 1.1.0 v1.1.0 criteria-combination framework: matched Rule17 (1 Benign.Stand Alone) with applied criteria: BA1 stand-alone benign, BS1 strong; maps to Benign.
ClinGen VHL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VHL Version 1.1.0 v1.1.0 criteria-combination framework: matched Rule17 (1 Benign.Stand Alone) with applied criteria: BA1 stand-alone benign, BS1 strong; maps to Benign.
Classification rationale
BA1BS1 Benign
VHL c.-77C>T

NM_000551.3:c.-77C>T meets BA1 (Stand-Alone) under VHL VCEP v1.1.0: GroupMax Filtering Allele Frequency of 8.88% in gnomAD v4.1 far exceeds the BA1 threshold of 0.0156%, establishing this variant as benign.1 NM_000551.3:c.-77C>T also meets BS1 (Strong): GroupMax Filtering Allele Frequency of 8.88% far exceeds the BS1 threshold of 0.00156%, further supporting a benign classification.2 NM_000551.3:c.-77C>T is observed in 332 homozygotes in gnomAD v4.1 and 36 homozygotes in gnomAD v2.1, incompatible with autosomal dominant von Hippel-Lindau disease with high penetrance.3 ClinVar classifies this variant as Benign (Variation ID 256649; 2 clinical laboratories) and Likely benign (1 clinical laboratory).4 No pathogenic or likely pathogenic criteria were met. PM2 was not met (frequency far exceeds PM2_Supporting threshold). PP3 was not met (no computational evidence of deleterious effect). PVS1, PS1, PM1, and PM5 are not applicable to this 5'UTR variant.5 Under VHL VCEP v1.1.0 combination rules (Rule 17), BA1 alone is sufficient for a Benign classification. Overall classification: Benign.6

BA1 + BS1 Benign
Gene diagram · NM_000551.3 · variants mapped to exon structure
VHL NM_000551.3
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 0.00492308; MAF= 0.49231%, 7326/1488092 alleles, homozygotes = 332) and has highest observed frequency in the African/African American population (AF= 0.0906683; MAF= 9.06683%, 6471/71370 alleles, homozygotes = 325); grpmax FAF= 0.0888216.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.0257254; MAF= 2.57254%, 805/31292 alleles, homozygotes = 36) and has highest observed frequency in the African/African American population (AF= 0.0908356; MAF= 9.08356%, 787/8664 alleles, homozygotes = 36); grpmax FAF= 0.0855752.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.49% · 7326 / 1,488,092
      332 hom · FAF 8.9%
      African/African American
      6471 / 71,370
      9.1%
      325 hom
      Admixed American
      320 / 49,082
      0.65%
      4 hom
      Remaining individuals
      367 / 57,666
      0.64%
      3 hom
      Middle Eastern
      9 / 4,228
      0.21%
      European (non-Finnish)
      153 / 1,098,908
      0.014%
      South Asian
      5 / 82,202
      0.0061%
      Ashkenazi Jewish
      1 / 27,836
      0.0036%
      + 3 not observed (European (Finnish), Amish, East Asian)
      gnomAD v2.1
      2.6% · 805 / 31,292
      36 hom · FAF 8.6%
      African/African American
      787 / 8,664
      9.1%
      36 hom
      Admixed American
      8 / 848
      0.94%
      Remaining individuals
      7 / 1,086
      0.64%
      European (non-Finnish)
      3 / 15,376
      0.02%
      + 4 not observed (Ashkenazi Jewish, East Asian, European (Finnish), South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (2 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 256649)
      SpliceAI screenshot
      In silico No data
      No in-silico prediction was recorded for this variant.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has previously been reported in somatic cancers (COSMIC; COSV104558409, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      7Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 9 PMIDs not cited in assessment
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      20301636 ↗ Von Hippel-Lindau Syndrome. CLINVAR
      20664475 ↗ The North American Neuroendocrine Tumor Society consensus guideline for the diagnosis and management of neuroendocrine tumors: pheochromocytoma, paraganglioma, and medullary thyroid cancer. CLINVAR
      23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
      24319509 ↗ Canadian guideline on genetic screening for hereditary renal cell cancers. CLINVAR
      25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      24893135 ↗ Pheochromocytoma and paraganglioma: an endocrine society clinical practice guideline. CLINVAR